He served his apprenticeship as a shipwright under Christopher Pett, Master Shipwright at Woolwich and one of the family which dominated the naval dockyards of the period. He rose rapidly, and was assistant master shipwright at Woolwich by 1660, at the age of twenty-two. Between 1660 and 1675 he designed and built twenty-five ships, more than a quarter of the ships added to the navy in those years, and he built sixteen out of forty-four of the larger or ‘rated’ ships.

1662 - met Samuel Pepys, who saw him as a possible rival for the Pett family of shipbuilders. 1664 - appointed master shipwright at Harwich upon its reopening, giving him his first chance to design and build ships. 1667 - became an officer in the militia. Built the seventy-gun Resolution, which Pepys described as ‘the best ship by report in all the world’. 1668 - promoted master shipwright of the Royal Dockyard at Portsmouth. 1670 - wrote the Doctrine of Naval Architecture, which gives the clearest account, before the eighteenth century, of how the hull of a warship was designed. 1671 - built the H.M.S. James Royal. 1672 - became commissioner at Portsmouth. 1673 - built the H.M.S. Charles Royal. 1674 - became a member of the Navy Board as commissioner of the victualling accounts. 1675 - knighted. Visited France on the orders of the king, to build two yachts for Louis XIV. 1679 - during the exclusion crisis, when he was accused of giving information to the French, he was imprisoned in the Tower of London with Pepys. 1681 - was elected to the Royal Society. 1686 - demanded a salary of £1000 to return to the navy as a member of a special commission for the repair of the fleet. 1689 - was once more imprisoned, along with Pepys. 1698 - during his visit to Deptford, Peter the Great took lessons from Deane on shipbuilding.